You need something to seal the clear coat, as clear coat paints are often porous. I spent a day treating my raw frame (unpainted, no clear) with naval jelly, and immediately followed it up with a coat of carnauba wax. Wax isn't ideal, as it needs to replied fairly frequently (once every couple of months), but it should hold me over til the summer when I plan to get it powder coated.
That being said, you should contact Eighth Inch and see if they'll do something about that. I wouldn't be too pleased if I received a new frame with that much rust on it.